rs207524

Variant names:

• chr21-23814172-C-A
• rs207524
• ENST00000807614.1:n.123+1435C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-23814172-C-A
• chr21-23814172-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807614.1(ENSG00000287612):​n.123+1435C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.972 in 151,630 control chromosomes in the GnomAD database, including 71,582 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.97 (71582 hom., cov: 31)
• Consequence: ENSG00000287612 ENST00000807614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

Genes affected

ENSG00000287612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807614.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287612	ENST00000807614.1		n.123+1435C>A		intron	N/A
	ENSG00000287612	ENST00000807615.1		n.126+1435C>A		intron	N/A
	ENSG00000287612	ENST00000807616.1		n.88+1435C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.972 AC: 147296 AN: 151514 Hom.: 71539 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.978

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.972 AC: 147397 AN: 151630 Hom.: 71582 Cov.: 31 AF XY: 0.973 AC XY: 72157 AN XY: 74128

African (AFR) AF: 0.904 AC: 37036 AN: 40948

American (AMR) AF: 0.988 AC: 15093 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3445 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5170

South Asian (SAS) AF: 0.998 AC: 4811 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10593 AN: 10594

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67979 AN: 68028

Other (OTH) AF: 0.977 AC: 2066 AN: 2114

Alfa AF: 0.703 Hom.: 2595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs207524;

hg19: chr21-25186489;